Open jesusdpa1 opened 4 years ago
Update:
Manage to debug some errors I had in the code, but started getting the following error: when using the following pipeline.sh
export PYTHONWARNINGS='ignore::FutureWarning:h5py,ignore:ImageJ tags do not contain "axes" property:UserWarning:main'
DATA_DIR=/lab/data/images/src_CX_19-002_spleen_CC2-A/ BASE_CONF=/lab/data/config/experiment.yaml
cytokit config editor --base-config-path=$BASE_CONF --output-dir=/lab/data/images/output \ add analysis '{"cellprofiler_quantification": {"export_db": True, "export_csv": True, "export_db_objects_separately": True}}' \ set environment.path_formats "get_default_path_formats('cyc{cycle:03d}reg001/{region:d}{tile:05d}_Z{z:03d}_CH{channel:d}.tif')" \ set processor.args.run_drift_comp True \ set processor.args.run_deconvolution True \ save_variant v00/config reset \ exit
OUTPUT_DIR=/lab/data/images/output/$VARIANT CONFIG_DIR=/lab/data/images/output/v00/config/experiment.yaml echo "Processing experiment $EXPERIMENT (variant = $VARIANT, config = $CONFIG_DIR)"
echo "Running analysis" cytokit processor run_all --config-path=$CONFIG_DIR --data-dir=$DATA_DIR --output-dir=$OUTPUT_DIR
When changing the data-dir in the pipeline:
cytokit processor run_all --config-path=$CONFIG_DIR --data-dir=$OUTPUT_DIR --output-dir=$OUTPUT_DIR
Thanks in advance for your help,
Ah, you should change "run_tile_generator: false" in the config to "run_tile_generator: true" if you're running on your own data. I updated that config to have a comment in the future for anyone else that copies it. Turning that off is only necessary when you can't get raw images for an experiment (as was the case with the CODEX publication) and have to use assembled hyperstacks instead, which is almost never, so there should have definitely been a comment about it.
Also, I'd suggest:
processor run_all
command at that instead (the "output" folder should be at the same level as "raw")run_deconvolution: false
to the processor.args property in the config)Hi Eric,
Thank you very much! I'll do the modifications to the path. After changing "run_tile_generator: true" it started working but gave me the following error:
from my experience I know that RTX have a problem handling memory allocation. The way I have been able to solve this problem is by limiting the usage of the memory to 0.8 of the total memory with
config = tf.ConfigProto() config.gpu_options.per_process_gpu_memory_fraction = 0.8 session = tf.Session(config=config)
is it possible to do this with cytokit? Do you think that I am presenting another problem?
Solved it. Had a bad math calculation
previous = tile_height: 1007 -> now = tile_height: 1008
But got the problem I was expecting on the GPU memory
Hi @jesusdpa1 ,
A couple thoughts:
run_crop: True
in the config (processor.args property) if the images overlap one another. That too was a quirk of analyzing non-raw data for the publication and will save precious GPU memory.Hi Eric,
Thank you very much! everything help, the program is now running smoothly,
Hi,
I am trying to run cytokit on our acquired data, but I am not able to set up the ylam correctly nor the processing bash file. we ran 9 group of antibodies, 10 Z planes and 49 sections
Here is what I got:
YLAM
experiment.txt
SH
pipeline_execution.txt
Error